Starting phenix.real_space_refine on Mon Sep 23 14:27:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/09_2024/7wlc_32581.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/09_2024/7wlc_32581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/09_2024/7wlc_32581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/09_2024/7wlc_32581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/09_2024/7wlc_32581.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wlc_32581/09_2024/7wlc_32581.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2094 2.51 5 N 563 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3307 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187} Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.43, per 1000 atoms: 0.73 Number of scatterers: 3307 At special positions: 0 Unit cell: (53.04, 80.08, 95.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 636 8.00 N 563 7.00 C 2094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 403.3 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 8.8% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.781A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 389 removed outlier: 3.657A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 386 through 389' Processing helix chain 'E' and resid 405 through 411 removed outlier: 4.535A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 411 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.569A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.730A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.730A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 391 through 392 removed outlier: 3.634A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 453 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.789A pdb=" N GLU H 10 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA H 118 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.625A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 23 100 hydrogen bonds defined for protein. 237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1071 1.34 - 1.47: 889 1.47 - 1.59: 1416 1.59 - 1.71: 0 1.71 - 1.84: 16 Bond restraints: 3392 Sorted by residual: bond pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB ASN E 448 " pdb=" CG ASN E 448 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" N GLY H 112 " pdb=" CA GLY H 112 " ideal model delta sigma weight residual 1.444 1.454 -0.010 9.60e-03 1.09e+04 9.95e-01 bond pdb=" C ASN E 331 " pdb=" N ILE E 332 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.40e-02 5.10e+03 9.85e-01 bond pdb=" CG LYS H 13 " pdb=" CD LYS H 13 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.82e-01 ... (remaining 3387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 4508 1.92 - 3.83: 86 3.83 - 5.75: 13 5.75 - 7.67: 5 7.67 - 9.59: 2 Bond angle restraints: 4614 Sorted by residual: angle pdb=" C ASN E 331 " pdb=" N ILE E 332 " pdb=" CA ILE E 332 " ideal model delta sigma weight residual 121.70 128.16 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA MET H 81 " pdb=" CB MET H 81 " pdb=" CG MET H 81 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CB LYS H 13 " pdb=" CG LYS H 13 " pdb=" CD LYS H 13 " ideal model delta sigma weight residual 111.30 119.20 -7.90 2.30e+00 1.89e-01 1.18e+01 angle pdb=" CB MET H 81 " pdb=" CG MET H 81 " pdb=" SD MET H 81 " ideal model delta sigma weight residual 112.70 103.11 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CA TRP H 111 " pdb=" CB TRP H 111 " pdb=" CG TRP H 111 " ideal model delta sigma weight residual 113.60 119.66 -6.06 1.90e+00 2.77e-01 1.02e+01 ... (remaining 4609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 1779 15.37 - 30.74: 175 30.74 - 46.11: 29 46.11 - 61.48: 13 61.48 - 76.85: 8 Dihedral angle restraints: 2004 sinusoidal: 768 harmonic: 1236 Sorted by residual: dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 28.64 64.36 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual 93.00 34.26 58.74 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CA MET H 81 " pdb=" C MET H 81 " pdb=" N GLU H 82 " pdb=" CA GLU H 82 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 2001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 244 0.028 - 0.056: 160 0.056 - 0.084: 57 0.084 - 0.111: 25 0.111 - 0.139: 11 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO E 373 " pdb=" N PRO E 373 " pdb=" C PRO E 373 " pdb=" CB PRO E 373 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE L 76 " pdb=" N ILE L 76 " pdb=" C ILE L 76 " pdb=" CB ILE L 76 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 494 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO L 60 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 111 " -0.015 2.00e-02 2.50e+03 9.52e-03 2.27e+00 pdb=" CG TRP H 111 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 111 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP H 111 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 111 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 111 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 111 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS E 336 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO E 337 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " 0.019 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 234 2.74 - 3.28: 3348 3.28 - 3.82: 5244 3.82 - 4.36: 5995 4.36 - 4.90: 10460 Nonbonded interactions: 25281 Sorted by model distance: nonbonded pdb=" O ASN E 448 " pdb=" OG SER E 494 " model vdw 2.198 3.040 nonbonded pdb=" NZ LYS H 23 " pdb=" O THR H 76 " model vdw 2.242 3.120 nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 115 " model vdw 2.263 3.040 nonbonded pdb=" O TYR H 108 " pdb=" OH TYR L 37 " model vdw 2.264 3.040 nonbonded pdb=" O ARG H 67 " pdb=" OG SER H 84 " model vdw 2.271 3.040 ... (remaining 25276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.130 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3392 Z= 0.193 Angle : 0.701 9.586 4614 Z= 0.378 Chirality : 0.044 0.139 497 Planarity : 0.005 0.039 601 Dihedral : 13.708 76.851 1202 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.42), residues: 424 helix: -3.38 (0.98), residues: 18 sheet: 0.25 (0.50), residues: 131 loop : -1.37 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 111 HIS 0.001 0.000 HIS H 110 PHE 0.021 0.002 PHE E 497 TYR 0.018 0.001 TYR E 351 ARG 0.006 0.000 ARG E 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 392 PHE cc_start: 0.8997 (m-80) cc_final: 0.8779 (m-80) REVERT: E 467 ASP cc_start: 0.7961 (t70) cc_final: 0.7735 (t0) REVERT: H 29 PHE cc_start: 0.7613 (t80) cc_final: 0.7264 (t80) REVERT: H 67 ARG cc_start: 0.8905 (ptp-170) cc_final: 0.8544 (ttp-110) REVERT: L 39 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7662 (tp-100) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1742 time to fit residues: 20.3233 Evaluate side-chains 80 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 50.0000 chunk 31 optimal weight: 0.0070 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 40.0000 chunk 32 optimal weight: 50.0000 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 30.0000 chunk 24 optimal weight: 40.0000 chunk 38 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 overall best weight: 3.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3392 Z= 0.192 Angle : 0.699 10.162 4614 Z= 0.359 Chirality : 0.047 0.140 497 Planarity : 0.005 0.039 601 Dihedral : 5.443 19.414 471 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.95 % Allowed : 13.93 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.42), residues: 424 helix: -3.51 (1.23), residues: 12 sheet: 0.24 (0.47), residues: 140 loop : -1.29 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 111 HIS 0.002 0.001 HIS H 110 PHE 0.023 0.002 PHE E 429 TYR 0.015 0.002 TYR E 449 ARG 0.007 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 346 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7520 (mtp85) REVERT: H 29 PHE cc_start: 0.7747 (t80) cc_final: 0.7287 (t80) REVERT: H 48 MET cc_start: 0.8275 (mmp) cc_final: 0.7648 (tpp) REVERT: H 67 ARG cc_start: 0.8827 (ptp-170) cc_final: 0.8564 (ttp-110) REVERT: L 39 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7654 (tp-100) REVERT: L 93 ASP cc_start: 0.7853 (t0) cc_final: 0.7649 (t0) outliers start: 7 outliers final: 4 residues processed: 84 average time/residue: 0.1765 time to fit residues: 17.5966 Evaluate side-chains 79 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 40.0000 chunk 25 optimal weight: 50.0000 chunk 10 optimal weight: 20.0000 chunk 38 optimal weight: 40.0000 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 50.0000 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 overall best weight: 9.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3392 Z= 0.274 Angle : 0.708 10.078 4614 Z= 0.364 Chirality : 0.047 0.154 497 Planarity : 0.005 0.041 601 Dihedral : 5.624 19.246 471 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.51 % Allowed : 15.88 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.42), residues: 424 helix: -3.12 (1.10), residues: 18 sheet: 0.21 (0.46), residues: 146 loop : -1.41 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.014 0.002 PHE H 64 TYR 0.016 0.002 TYR E 365 ARG 0.006 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7949 (t80) cc_final: 0.7456 (t80) REVERT: H 48 MET cc_start: 0.8280 (mmp) cc_final: 0.7866 (mmm) REVERT: H 67 ARG cc_start: 0.8768 (ptp-170) cc_final: 0.8524 (ttp-110) REVERT: L 36 TRP cc_start: 0.7549 (m100) cc_final: 0.7166 (m100) REVERT: L 46 LYS cc_start: 0.9353 (tppp) cc_final: 0.9134 (tppp) outliers start: 9 outliers final: 7 residues processed: 85 average time/residue: 0.1785 time to fit residues: 17.9527 Evaluate side-chains 87 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 40 optimal weight: 50.0000 chunk 20 optimal weight: 40.0000 chunk 36 optimal weight: 40.0000 chunk 10 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 overall best weight: 13.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3392 Z= 0.350 Angle : 0.766 11.017 4614 Z= 0.401 Chirality : 0.048 0.150 497 Planarity : 0.005 0.043 601 Dihedral : 6.006 20.130 471 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 3.34 % Allowed : 18.66 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.40), residues: 424 helix: -3.31 (1.01), residues: 18 sheet: 0.01 (0.47), residues: 141 loop : -1.62 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.023 0.003 PHE E 338 TYR 0.015 0.002 TYR L 86 ARG 0.005 0.001 ARG E 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 346 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7847 (mtp85) REVERT: H 29 PHE cc_start: 0.8083 (t80) cc_final: 0.7593 (t80) REVERT: H 48 MET cc_start: 0.8288 (mmp) cc_final: 0.7721 (mmm) REVERT: H 67 ARG cc_start: 0.8841 (ptp-170) cc_final: 0.8556 (ttp-110) REVERT: L 36 TRP cc_start: 0.7741 (m100) cc_final: 0.7506 (m100) REVERT: L 39 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7628 (tp-100) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 0.1979 time to fit residues: 19.7137 Evaluate side-chains 89 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 40.0000 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3392 Z= 0.253 Angle : 0.731 11.946 4614 Z= 0.373 Chirality : 0.047 0.140 497 Planarity : 0.005 0.043 601 Dihedral : 5.767 19.727 471 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.62 % Allowed : 19.50 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.41), residues: 424 helix: -3.21 (1.02), residues: 18 sheet: -0.01 (0.47), residues: 140 loop : -1.48 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.013 0.002 PHE E 338 TYR 0.013 0.002 TYR L 86 ARG 0.005 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 474 GLN cc_start: 0.2844 (pp30) cc_final: 0.2448 (pp30) REVERT: H 29 PHE cc_start: 0.7972 (t80) cc_final: 0.7439 (t80) REVERT: H 48 MET cc_start: 0.8167 (mmp) cc_final: 0.7725 (mmm) REVERT: H 67 ARG cc_start: 0.8798 (ptp-170) cc_final: 0.8545 (ttp-110) REVERT: L 39 GLN cc_start: 0.7902 (tp-100) cc_final: 0.7615 (tp-100) REVERT: L 93 ASP cc_start: 0.8043 (t0) cc_final: 0.7840 (t0) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 0.1933 time to fit residues: 20.7671 Evaluate side-chains 92 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 20.0000 chunk 40 optimal weight: 50.0000 chunk 33 optimal weight: 40.0000 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 21 optimal weight: 50.0000 chunk 39 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 overall best weight: 14.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 3392 Z= 0.378 Angle : 0.786 11.480 4614 Z= 0.408 Chirality : 0.048 0.157 497 Planarity : 0.005 0.047 601 Dihedral : 6.146 20.189 471 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 4.18 % Allowed : 21.45 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.40), residues: 424 helix: -3.42 (0.95), residues: 18 sheet: -0.17 (0.47), residues: 141 loop : -1.61 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 111 HIS 0.004 0.001 HIS H 110 PHE 0.020 0.003 PHE E 392 TYR 0.016 0.002 TYR E 351 ARG 0.005 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 346 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7662 (mtp85) REVERT: H 29 PHE cc_start: 0.8161 (t80) cc_final: 0.7551 (t80) REVERT: H 48 MET cc_start: 0.8182 (mmp) cc_final: 0.7692 (mmm) REVERT: L 46 LYS cc_start: 0.9561 (tppp) cc_final: 0.9336 (tppp) REVERT: L 93 ASP cc_start: 0.8092 (t0) cc_final: 0.7869 (t0) outliers start: 15 outliers final: 13 residues processed: 88 average time/residue: 0.2027 time to fit residues: 21.0768 Evaluate side-chains 91 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 40.0000 chunk 34 optimal weight: 30.0000 chunk 40 optimal weight: 40.0000 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3392 Z= 0.243 Angle : 0.734 12.049 4614 Z= 0.373 Chirality : 0.047 0.144 497 Planarity : 0.005 0.047 601 Dihedral : 5.806 20.824 471 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.90 % Allowed : 22.56 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.41), residues: 424 helix: -3.24 (1.05), residues: 18 sheet: -0.19 (0.47), residues: 141 loop : -1.51 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.011 0.002 PHE E 374 TYR 0.022 0.002 TYR E 351 ARG 0.005 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.8068 (t80) cc_final: 0.7374 (t80) REVERT: H 48 MET cc_start: 0.8150 (mmp) cc_final: 0.7718 (mmm) REVERT: L 93 ASP cc_start: 0.8184 (t0) cc_final: 0.7949 (t0) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.1846 time to fit residues: 19.1855 Evaluate side-chains 90 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 20.0000 chunk 31 optimal weight: 0.0040 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 50.0000 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 11 optimal weight: 0.0060 chunk 34 optimal weight: 40.0000 overall best weight: 3.9414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3392 Z= 0.192 Angle : 0.712 8.783 4614 Z= 0.363 Chirality : 0.047 0.152 497 Planarity : 0.005 0.046 601 Dihedral : 5.607 22.818 471 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.79 % Allowed : 24.79 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.41), residues: 424 helix: -3.17 (1.04), residues: 18 sheet: -0.11 (0.48), residues: 136 loop : -1.29 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.020 0.002 PHE E 374 TYR 0.021 0.002 TYR E 351 ARG 0.007 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7935 (t80) cc_final: 0.7153 (t80) REVERT: H 48 MET cc_start: 0.8055 (mmp) cc_final: 0.7643 (mmm) outliers start: 10 outliers final: 8 residues processed: 93 average time/residue: 0.1695 time to fit residues: 18.8902 Evaluate side-chains 87 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 40.0000 chunk 33 optimal weight: 50.0000 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3392 Z= 0.206 Angle : 0.742 11.305 4614 Z= 0.375 Chirality : 0.047 0.145 497 Planarity : 0.005 0.046 601 Dihedral : 5.543 23.670 471 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.79 % Allowed : 26.74 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.41), residues: 424 helix: -3.63 (0.95), residues: 18 sheet: -0.10 (0.47), residues: 141 loop : -1.28 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.021 0.002 PHE E 497 TYR 0.021 0.002 TYR E 351 ARG 0.007 0.001 ARG L 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7925 (t80) cc_final: 0.7176 (t80) REVERT: H 48 MET cc_start: 0.8049 (mmp) cc_final: 0.7509 (tpp) outliers start: 10 outliers final: 10 residues processed: 88 average time/residue: 0.1922 time to fit residues: 19.7959 Evaluate side-chains 92 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 40.0000 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 33 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 overall best weight: 6.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3392 Z= 0.236 Angle : 0.775 12.258 4614 Z= 0.393 Chirality : 0.047 0.148 497 Planarity : 0.005 0.047 601 Dihedral : 5.588 23.077 471 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.79 % Allowed : 27.30 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.41), residues: 424 helix: -3.63 (0.96), residues: 18 sheet: -0.06 (0.48), residues: 132 loop : -1.27 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.023 0.002 PHE E 497 TYR 0.022 0.002 TYR E 351 ARG 0.007 0.001 ARG E 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 392 PHE cc_start: 0.8905 (m-80) cc_final: 0.8656 (m-10) REVERT: H 29 PHE cc_start: 0.7927 (t80) cc_final: 0.7172 (t80) REVERT: H 48 MET cc_start: 0.8027 (mmp) cc_final: 0.7658 (mmm) REVERT: H 80 TYR cc_start: 0.8164 (m-80) cc_final: 0.7846 (m-80) outliers start: 10 outliers final: 10 residues processed: 87 average time/residue: 0.1810 time to fit residues: 18.7247 Evaluate side-chains 91 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 96 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 40.0000 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 22 optimal weight: 50.0000 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.127610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098488 restraints weight = 8962.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.101277 restraints weight = 5407.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.103175 restraints weight = 3841.424| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3392 Z= 0.230 Angle : 0.768 12.078 4614 Z= 0.388 Chirality : 0.047 0.150 497 Planarity : 0.005 0.047 601 Dihedral : 5.575 22.767 471 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.06 % Allowed : 26.74 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.41), residues: 424 helix: -3.62 (0.96), residues: 18 sheet: -0.14 (0.47), residues: 140 loop : -1.27 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 111 HIS 0.005 0.001 HIS H 110 PHE 0.022 0.002 PHE E 374 TYR 0.022 0.002 TYR E 351 ARG 0.006 0.001 ARG L 17 =============================================================================== Job complete usr+sys time: 1036.14 seconds wall clock time: 19 minutes 34.36 seconds (1174.36 seconds total)